The latest endeca ATG integrated module donot use developer studio for configuring record adaptor.
I would like to know how to configure and index third party data source with JDBC connection or csv file or even craweld content.

You can still update a forge-based pipeline in Dev Studio and add additional record adapters (or you can add them as data sources in CAS). You'll have some record adapters in your pipeline that pull from the CAS record stores populated by the ATG-Endeca integration.